Proteins are responsible for coding an organism’s traits. A genetic code will define how sequences of nucleotide triplets known as codons will determine the sequence of amino acids during protein synthesis. In general there are three nucleotide codons in nucleic acid sequences that will create one amino acid, though there are some exceptions to this rule. Most genes use the same RNA codon table to create these patterns, known as the standard genetic code, which is altered based on the specifications needed for a given organism.
Not all genetic information is transmitted or stored within the genetic code. DNA contains sequences that can be used for regulating this process as well as chromosomal structural areas, intergenic segments and non-coding DNA that is used to phenotype different types of cells. These elements follow a separate set of rules that is not within the codon amino acid paradigm that helps to regulate the genetic code.
The genomes of organisms are typically stored in the DNA, though viruses contain this information in the RNA, which is used to code the proteins for different genes.
- Genes that are coded for proteins contain tri-nucleotide codons that contain the instructions for an amino acid. Each of these sub-units contains a deoxyribose sugar, a phosphate and one of four different nucleobases, guanine, adenine, cytosine or thymine.
- The double helix of DNA joins two strands together using hydrogen bonds in a base paring. These bands typically match thymine with adenine and guanine with cytosine. RNA matches thymine with uracil and contains ribose instead of deoxyribose.
- The coded proteins are transcribed onto molecules with the RNA polymer. In prokaryote the RNA will act as mRNA and ribosomes will act on a chain of amino acids known as polypeptides. This process of transferring RNA to a certain amino acid is powered by guanosine triphsosphate and requires a number of factors to allow for translation. tRNA must be provided with complementary anticodons to the mRNA so it can be covalently charged with the amino acids at their CCA ends by aminoacyl tRNA synthetases. This has a high specificity rate for the cognate amino acids and the tRNA alike which is one of the major reasons why these enzymes are capable of maintaining the translation of the protein sequences.
Different amino acids can be encoded with up to six different codon sequences. This can be compared to using bioinformatics, comparing codons to different words or a piece of data that is necessary to create a whole message. In this example a nucleotide would be a bit, or the smallest possible unit that can be used to make a functional message.
This allows for a wide degree of variation both between different kinds of organisms and within the same species. High amounts of variation ensure that organisms are able to adapt to their environment, helping to ensure survival over time.
Varying the Genetic Code
Slight variations in the genetic code have been predicted as early as 1979 with the study of mitochondrial genes.
- Since this discovery a variety of alterations to the mitochondrial code, both large and small, have been discovered.
- Viruses use the same genetic code as the organism that is acting as their host, so being able to predict and modify the genetic code of an organism could interfere with their ability to function. However, there are some types of viruses that are able to work within the modification of a genetic code in their hosts. Some bacteria or archaea use common start codons and alter the proteins used by the species that they invade to get around this as well.
- Some proteins can be substituted for the standard stop codons depending on how the messenger RNA interacts with these sequences. This allows different codes to be expressed simultaneously in a single organism, creating a difference in their growth conditions. In spite of this, the codes in these organisms will be very similar. All coding mechanisms contain a reading code and tRNA ribosomes that move in the same direction and translate the code into amino acids three units at a time.
- Given these alterations in coding, 40 unnatural amino acids have been added to the protein sequence to create unique codons since 2001.
Some predictions to the genetic code can be performed if the genes encoded on a particular genome can be identified. If researchers compare the DNA from some amino acids to the proteins in other genomes, they can get an idea of how these traits will be displayed. Evolution conserves protein sequences, which helps make it possible for observers to predict how amino acids will be translated from different codons.
A program called FACIL can be used to automatically predict different expressions of the genetic code by seeking out different amino acids in a homologous protein domain and how they are aligned with the codons.
Mutations and Errors
During DNA replication you may occasionally see errors known as mutations that occur as the second strand polymerizes.
- Mutations can impact the development of the phenotype of an organism, particularly if the protein code sequence was affected by this change. These mutations occur around once every 10 or 100 million times during polymerization based on the ability of the polyerases to perform this function.
- If a mutation disrupts the frame sequence it can result in a very difference cell from the original, impairing the protein and causing in vivo alterations in coding. A properly encoded protein sequence is essential for the proper growth of the organism to ensure that it will be able to survive against different challenges it will face in the environment, so alterations in the protein sequence can often result in the organism dying before it becomes viable. Therefore the inheritance of a mutation is quite rare.
- In some cases a mutation can result in a genetic disease being inherited such as Down’s syndrome in humans. These types of occurrences typically prevent the organism from reproducing, limiting the chances that these traits can be passed on.
- Some alterations to the protein sequence do not do any harm, or even have a positive effect, allowing the organism to better withstand new changes to their environment or reproduce at a better rate. In this case these traits will be passed on more quickly, causing a change in the population of organisms as a whole. This process is known as natural selection.
Though not always considered a form of life, viruses use this mechanism as a means of survival. Their RNA is capable of mutating very quickly, allowing it to work around the immune system of the animals where it invades. When working with large groups of organisms like E. coli that reproduce very quickly using asexual means a mutation can be helpful for ensuring survival. This is known as clonal interface which causes a high amount of competition in organisms.
There is also a phenomenon known as degeneracy that refers to the redundancy of the genetic code which causes a lack of ambiguity. This may be helpful to an organism if some errors in their genetic code cause a silent mutation that does not affect the structure of the proteins because the overall hydrophobicity or hydrophilicity is kept equal by substituting the position of amino acids. These types of errors can lead to a shared ancestry of tRNA synthetases that are related to the patterns created by the codons.